At a time when the rate of unaccompanied children crossing the southern U.S. border without parents or guardians has skyrocketed 90 percent since last year and many are sleeping in crowded conditions in federal facilities, five major human rights groups has filed a joint complaint on behalf of 116 unaccompanied children who were reportedly abused by Customs and Border Protection (CBP) agency officials and Border Patrol agents.

One in four unaccompanied alien children included in the complaint reported some form of physical abuse, like sexual assault, beatings, and the use of stress positions by CBP officials. More than half of those children also reported some form of verbal abuse. A majority also reported being denied adequate food, water, and medical care, like CBP officials withholding formula for young mothers with infant children and and confiscating asthma medication even after a child suffered multiple asthma attacks. At least 70 percent of children reported that they were held beyond the “legally-mandated 72-hour period.”

Some of those abuse allegations from children between the ages of five and 17 include a seven-year-old, developmentally disabled boy, who was held in custody for five days without medical treatment. A 16-year-old girl was not only detained with adults, but CBP officials “violently spread her legs and touched her genital area forcefully, making her scream.” A 14-year-old girl had her asthma medication confiscated and after her first asthma attack, “officials threatened that they would punish her if she were faking.” One 16-year-old boy said that he was made to walk without his shoes to the detention facility where one CBP official threatened, “you are in my country now, and we are going to bury you in a hole.”

One of the limitations that the report acknowledged was that the number of children who were mistreated are only a “representative sample and not an exhaustive compilation” since they might have declined to file a complaint for fear that “doing so would negatively impact their immigration case or otherwise result in retaliation.” According to CNN, the Department of Homeland Security (DHS) “wouldn’t comment on whether it was investigating the allegations.”

James Lyall, an ACLU Border Litigation Staff Attorney, told ThinkProgress on Friday that the majority of the cases included in the complaint were documented “between March and May 2014, but the abuses happened earlier. These abuses are not the result of the large [numbers] of children, though that humanitarian crisis only makes the need for major CBP reforms all the more urgent, as more children are coming into contact w/ more CBP officials for longer periods of time, with no oversight, accountability or transparency – the current situation as it stands is a recipe for further abuse of vulnerable children.”

The organizations involved in the complaint include the ACLU Border Litigation Project, the National Immigrant Justice Center (NIJC), Esperanza Immigrant Rights Project, Americans for Immigrant Justice, Florence Immigrant and the Refugee Rights Project.

More than 60,000 unaccompanied migrant children are expected to cross the southern border into the United States this year in search of a safer life. Some are trying to reunite with their relatives while others are fleeing violence in El Salvador, Guatemala, and Honduras.

While CBP officials recently stated that the agency was doing its best to move children out of its facilities within 72 hours, the agency has otherwise struggled to maintain a public image that’s aligned with its mission to be more transparent and less aggressive towards detainees. On Monday, the CBP agency reassigned its head of internal affairs, James Tomscheck, with some senior officials telling the Los Angeles Times that he “directed agents away from investigating individual cases of alleged wrongdoing.” Last month, the American Immigration Council uncovered that “no action” was taken by border officials in 97 percent of complaints filed through nine southwestern sectors between 2009 and 2012 fiscal years.

This is not the first time that unaccompanied children have alleged that CBP has abused them. In 2009, the Florence Project interviewed 124 unaccompanied children, 85 percent of whom complained of “excessively cold” holding cells. That report found 18 specific cases of physical abuse and 16 cases of verbal abuse. In 2011, No More Deaths (NMD) found 30,000 abuse allegations against adult and child immigrants in short-term CBP custody. The complaint found that “particularly troubling is the failure of DHS oversight agencies to respond to these reports.” Children transferred from CBP facilities to shelters operated by the Office of Refugee Resettlement (ORR) are similarly vulnerable. Just last month, the Houston Chronicle found that at least 101 unaccompanied children were allegedly abused by ORR officials.

Lyall said, “While CBP taking the unusual step of promptly and publicly ordering an investigation is a welcome development, we continue to have real concerns about CBP’s demonstrated inability to police itself and believe independent oversight remains sorely lacking at DHS.”